{"id":"https://openalex.org/W4231838285","doi":"https://doi.org/10.1109/csb.2004.1332462","title":"Search-space reduction of a non-redundant peptide database","display_name":"Search-space reduction of a non-redundant peptide database","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W4231838285","doi":"https://doi.org/10.1109/csb.2004.1332462"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332462","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332462","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011206026","display_name":"I. Shadforth","orcid":null},"institutions":[{"id":"https://openalex.org/I82284825","display_name":"Cranfield University","ror":"https://ror.org/05cncd958","country_code":"GB","type":"education","lineage":["https://openalex.org/I82284825"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"I. Shadforth","raw_affiliation_strings":["Cranfield University, UK"],"affiliations":[{"raw_affiliation_string":"Cranfield University, UK","institution_ids":["https://openalex.org/I82284825"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088682730","display_name":"D. Crowther","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099842","display_name":"GlaxoSmithKline (India)","ror":"https://ror.org/01tvt4d48","country_code":"IN","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210099842"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"D. Crowther","raw_affiliation_strings":["Glaxo SmithKline"],"affiliations":[{"raw_affiliation_string":"Glaxo SmithKline","institution_ids":["https://openalex.org/I4210099842"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009753935","display_name":"C. Bessant","orcid":null},"institutions":[{"id":"https://openalex.org/I82284825","display_name":"Cranfield University","ror":"https://ror.org/05cncd958","country_code":"GB","type":"education","lineage":["https://openalex.org/I82284825"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"C. Bessant","raw_affiliation_strings":["Cranfield University, UK"],"affiliations":[{"raw_affiliation_string":"Cranfield University, UK","institution_ids":["https://openalex.org/I82284825"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011206026"],"corresponding_institution_ids":["https://openalex.org/I82284825"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.83673469,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"450","last_page":"451"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.702668309211731},{"id":"https://openalex.org/keywords/database-search-engine","display_name":"Database search engine","score":0.6851196885108948},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.6250171065330505},{"id":"https://openalex.org/keywords/tandem-mass-spectrometry","display_name":"Tandem mass spectrometry","score":0.5613700151443481},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.46813854575157166},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4549122154712677},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.42703384160995483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40760624408721924},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4010922610759735},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35634493827819824},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.24991393089294434},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.1875835359096527},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1815311312675476},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16543909907341003},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.08628404140472412}],"concepts":[{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.702668309211731},{"id":"https://openalex.org/C48000682","wikidata":"https://www.wikidata.org/wiki/Q5227411","display_name":"Database search engine","level":3,"score":0.6851196885108948},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.6250171065330505},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.5613700151443481},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.46813854575157166},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4549122154712677},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.42703384160995483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40760624408721924},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4010922610759735},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35634493827819824},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.24991393089294434},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.1875835359096527},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1815311312675476},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16543909907341003},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.08628404140472412},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/csb.2004.1332462","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332462","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},{"id":"pmh:oai:discovery.dundee.ac.uk:openaire_cris_publications/9f6f9448-f33a-4017-b9ef-33864f26606e","is_oa":false,"landing_page_url":"https://discovery.dundee.ac.uk/en/publications/9f6f9448-f33a-4017-b9ef-33864f26606e","pdf_url":null,"source":{"id":"https://openalex.org/S4306400523","display_name":"Discovery Research Portal (University of Dundee)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177639307","host_organization_name":"University of Dundee","host_organization_lineage":["https://openalex.org/I177639307"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Shadforth, I, Crowther, D & Bessant, C 2004, Search-space reduction of a non-redundant peptide database. in Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, pp. 470-471, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, United States, 16/08/04. https://doi.org/10.1109/CSB.2004.1332462","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W265487301","https://openalex.org/W2026465178","https://openalex.org/W2102329829"],"related_works":["https://openalex.org/W2393806059","https://openalex.org/W2143537935","https://openalex.org/W1589975312","https://openalex.org/W2103021125","https://openalex.org/W3210150956","https://openalex.org/W2582797103","https://openalex.org/W2046677260","https://openalex.org/W1999832194","https://openalex.org/W2051901836","https://openalex.org/W2073366206"],"abstract_inverted_index":{"Peptide":[0],"mass":[1,8,68],"fingerprinting":[2],"and":[3,105,121],"database":[4],"searching":[5],"with":[6],"tandem":[7,67],"spectrometry":[9],"are":[10,72,115],"two":[11],"methods":[12],"commonly":[13],"employed":[14],"to":[15,23,74,96],"identify":[16],"proteins":[17],"in":[18,117],"a":[19,33,41,50,82,139],"sample.":[20],"However,":[21],"up":[22],"90%":[24],"of":[25,53,62,78,88,119,123,132],"peptides":[26,79],"can":[27,93],"remain":[28],"unidentified.":[29],"In":[30],"this":[31,136],"paper,":[32],"search-space":[34],"filter":[35],"using":[36],"amino":[37,54,63,91,112],"acids":[38],"identified":[39],"by":[40,101],"novel":[42],"de":[43],"nova":[44],"methodology":[45],"is":[46],"presented.":[47],"This":[48],"provides":[49],"high-accuracy":[51],"set":[52],"acid":[55,64,92,113],"predictions":[56,71],"through":[57],"exploiting":[58],"the":[59,76,98,129],"internal":[60],"fragmentation":[61],"chains":[65],"during":[66],"spectrometry.":[69],"These":[70],"used":[73,95],"reduce":[75,97],"number":[77],"considered":[80],"from":[81],"non-redundant":[83],"peptide":[84,125,144],"database.":[85],"The":[86],"presence":[87],"one":[89],"confirmed":[90],"be":[94],"search-database":[99],"size":[100],"between":[102],"33%":[103],"(leucine)":[104],"83%":[106],"(tryptophan).":[107],"One":[108],"or":[109],"more":[110],"accurate":[111],"identifications":[114],"made":[116],"18%":[118],"simulated":[120],"9%":[122],"experimental":[124],"spectra":[126],"considered.":[127],"Given":[128],"large":[130],"proportion":[131],"currently":[133],"unidentified":[134],"peptides,":[135],"method":[137],"represents":[138],"useful":[140],"tool":[141],"for":[142],"increasing":[143],"identification":[145],"rates.":[146]},"counts_by_year":[],"updated_date":"2026-03-15T09:29:46.208133","created_date":"2025-10-10T00:00:00"}